ACHMAD FARAJALLAH
Departemen Biologi, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Institut Pertanian Bogor, Kampus Dramaga Bogor, Indonesia

Published : 47 Documents Claim Missing Document
Claim Missing Document
Check
Articles

Testing Reliability of Serum Samples as a DNA Source on Captive Breeding Long-tailed Macaques (Macaca fascicularis) Dyah Perwitasari-Farajallah; Achmad Farajallah
BIOTROPIA - The Southeast Asian Journal of Tropical Biology Vol. 21 No. 2 (2014)
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (126.976 KB) | DOI: 10.11598/btb.2014.21.2.306

Abstract

The serum realibility was tested in captive breeding conditions on the long-tailed macaques (Macaca fascicularis). Serum and buffy coat were applied to standard protocol of DNA extration following the amplification of microsatellite DNA locus of D2S1777 by PCR and visualized PCR products by means of PAGE with silver staining.  The amount of genomic DNA extracted from serum was sufficient for genotyping individuals at DNA microsatellite locus of D2S1777 with the allele size is approximately 160 bp.  We show that serum can provide a reliable alternative for obtaining DNA where taking blood using anticoagulant is impracticable
Kejadian Indel Simultan pada Intron 7 Gen Branched-Chain α-Ketoacid Dehydrogenase E1a (BCKDHA) pada Sapi Madura Asri Febriana; Achmad Farajallah; Dyah Perwitasari
Jurnal Ilmu Pertanian Indonesia Vol. 20 No. 2 (2015): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1157.4 KB) | DOI: 10.18343/jipi.20.2.97

Abstract

Madura cattle is one of the Indonesian local cattle breeds derived from crossing between Zebu cattle (Bos indicus) and banteng (Bos javanicus). Branched-chain α-ketoacid dehydrogenase (BCKDH) is one of the main enzyme complexes in the inner mitochondrial membrane that metabolizes branched chain amino acid (BCAA), ie valine, leucine, and isoleucine. The diversity of the nucleotide sequences of the genes largely determine the efficiency of enzyme encoded. This paper aimed to determine the nucleotide variation contained in section  intron 7, exon 8, and intron 8 genes BCKDHA on Madura cattle. This study was conducted on three Madura cattle that used as bull race (karapan), beauty contest (sonok), and beef cattle. The analysis showed that the variation in intron higher than occurred in the exon. Simultaneous indel found at base position 34 and 68 in sonok cattle. In addition, the C266T variant found in beef cattle. These variants do not cause significant changes in amino acids. There was no specific mutation in intron 7, exon 8, and intron 8 were found in Madura cattle designation. This indicated the absence of differentiation Madura cattle designation of selection pressure of BCKDHA gene.
Variasi Genetik Gen Myostatin Ekson 3 pada Sembilan Bangsa Kambing Lokal di Indonesia Rissa Herawati Ginting; Achmad Farajallah; Dyah Perwitasari Farajallah; Aron Batubara
Jurnal Ilmu Pertanian Indonesia Vol. 22 No. 2 (2017): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (523.264 KB) | DOI: 10.18343/jipi.22.2.73

Abstract

Myostatin gene plays a role in helping to control the growth and development of muscle tissue. Identification of genetic diversity in nine local goat breeds in Indonesia has done. The aim of this study was to obtain information myostatin gene diversity of exon 3 in local goats in Indonesia. The total of 10 samples was selected from 80 samples of goat's blood collected comprising each sample of the population of goats breeds, i.e., Samosir, Muara, Kacang, Costa, Peranakan Etawah, Boerawa, Gembrong, Boer, and Boerka goats. The gene diversity and nucleotide base changes were identified by using polymerase chain reaction (PCR) and sequencing techniques. The analysis showed that there is eight variant identified in appropriate with those found in sequencing results. Deletion variations were found in Costa and Samosir goats in T552- and G560-. Substitution variations were found in Gembrong (A7C & A11T), Peranakan Etawah (T10A & A11T), Burawa (T10A & A11T), Muara (A11T), Samosir (A11T), and Boerka (A182T, T437A, T439A, & A445G). Variations on the chromatogram peak overlapping contained in the base position to 13. Analysis of variance showed that there was a special mutation in exon 3 that affects the amino acid tyrosine into lysine. Variants were found in nine goat breeds associated with phylogenetic and genetic distance of goats, Boerka goat has the highest level of genetic variation, it indicated that Boerka goat was crossbreed
Polymorphism of Pituitary-Specific Transcription Factor-1 (Pit-1) Gene at Locus (Pit-1-Hinf1) and its effects on dam body weight and milk production of local sheeps Rahmat, D.; Farajallah, A.; Herdiana, D.; Sumantri, C.
Indonesian Journal of Animal and Veterinary Sciences Vol 14, No 3 (2009)
Publisher : Indonesian Animal Sciences Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (302.36 KB) | DOI: 10.14334/jitv.v14i3.344

Abstract

Pituitary-Specific Transcription Factor-1 (Pit-1) is a transcription factor with critical role in the transcriptional regulation of multiple genes in the pituitary. The objective of this research was to identify polymorphism of Pituitary-Specific Transcription Factor-1 (Pit-1) gene at Locus (Pit-1-Hinf1) and to investigate any possible associations of Pit-1 genotypes on dam body weight, milk production and milk quality in local sheep at the Jonggol Animal Science Teaching and Research Unit (JASTRU), Fact. Anim. Sci. Bogor. Agric. Univ. A total number of 161 blood samples were collected from 3 local sheep, namely Garut from Wanaraja (55 hd), Garut from Margawati (23 hd) and lactating ewes (83 hd) from JASTRU  farm in Bogor. Genomic DNAs were extracted by a standard phenol-chloroform protocol and amplified by a polymerase chain reaction (PCR) techniques, then PCR products were digested with a Hinf1 enzyme restriction. Fragments of Pit-1gene at locus Pit-1-Hinf1 was detected by a silver-staining method. A length of 637 base pairs (bps) of the Pit-1 gene of local sheep was successfully amplified. The Hinf1 restriction enzyme cut the PCR product into three different length of fragments succesively at 345, 137, and 115   bps designated as A allele; whilst B allele had four fragments at 283, 137, 115, and 62 bps respectively. The locus of Pit-1-Hinf1 was polymorphic in local sheep from Jonggol, however it was monomorfic in Garut sheep. The frequencies of A and B alleles were 0,806 and 0,194 respectively. Pit-1 genotypes had no significant effect on dam body weight and milk production. This result is indicating that the use of single locus Pit-1-Hinf1 in Pit-1 gen is less effective to be used as a candidate in selecting dam body weight and milk production in these three local sheep. Key words: Local Sheep, Pit-1 Gene, Polymorphism, Dam, Milk
Verification for the control of kappa-casein gene on milk protein yield of friesian-holstein in dairy central region of West Java Andreas, E.; Farajallah, A.; Sumantri, C.; Anggraeni, A.
Indonesian Journal of Animal and Veterinary Sciences Vol 14, No 2 (2009)
Publisher : Indonesian Animal Sciences Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (202.262 KB) | DOI: 10.14334/jitv.v14i2.354

Abstract

Genotipe of BB kappa kasein (ĸ-kasein) gene positively influences high milk protein yield. The aim of this research was to verify the use of the к-casein gene as marker of assisted selecion (MAS) of high protein yield in domestic Holstein-Friesian (HF) cattle. Genotyping blood samples was conducted for lactating cows from BPPT-SP Cikole (82 head) and a number of small holders in KPSBU Lembang (190 head). Genotyping the к-casein gene was also conducted for active and non active AI bulls (HF) from BIB Lembang (25 head) and BBIB Singosari (32 head). Varian genotipes were identified trough DNA migration, whereas frequencies of alleles were calculated by Nei Method (1987). The effects of variant genotypes on protein yield and other milk component yields were studied in lactating cows (56 head in BPPT-SP Cikole and 111 head in KPSBU Lembang) by applying Least Square Means (LSM) method of the General Linear Model (GLM). Genotyping the ĸ-kasein gene resulted in three genotypes, namely AA, AB and BB, with two alleles, namely A and B. It was identified that a very limited number of lactating cows with BB genotype (0-9%). These cows produced higher protein yield around 3.37-3.84% than that of AA cows, while AB cows produced protein yield in between, though these differences were not statistically significant (P>0,05). In contrast, AA cows tended to produced higher milk fat yield than BB cows. Cows BB and AB seemingly produced higher dry matter, while both specific density and pH were not affected by variant genotypes of the к-casein gene.  The results showed that BB genotype of the к-casein gene tended to be quitely consistent in controlling high protein yield, so it would be a good oppurtinity to be used as MAS of milk protein yield in HF domestic. Key words: Protein Yield, Dairy Cattle (HF), к-Casein Gene, Genotype BB
IDENTIFICATION OF GH|ALUI AND GHR|ALUI GENES POLYMORPHISMS IN INDONESIAN BUFFALO Andreas, E.; Sumantri, C.; Nuraini, H.; Farajallah, A.; Anggraeni, A.
Journal of the Indonesian Tropical Animal Agriculture Vol 35, No 4 (2010): (December)
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.35.4.215-221

Abstract

Growth hormone (GH) is an anabolic hormone which sintesized and secreted by somatrotop cell inpituitary anterior lobe. GH exert its effect on growth and metabolism by interacting with a specificreceptor on the surface of the target cells. Growth hormone receptor (GHR) has been suggested ascandidate gene for traits related to meat production in Bovidae. The objectives of this study were toidentify polymorphism of GH and GHR genes in buffalo. The 452 DNA samples buffalo were collectedfrom five populations in Indonesia (Siborong-Borong-Medan (65), Lebak-Banten (29), Pandeglang-Banten (180), Semarang-Central Java, and Mataram-West Nusa Tenggara (103)). A gene fragment of theGH|AluI gene at 432 bp located on exon 3 and GHR|AluI gene at 298 bp on exon 10 were successfullyamplified by using the techniques of a PCR (polymerase chain reaction) and genotyped by PCR-RFLP(restriction fragment length polymorphism) then -SSCP (single strand conformation polymorphism). Theresults showed no polymorphisms were detected in these genes. All buffaloes tested had LL genotype forlocus GH|AluI and AA genotype for locus GHR|AluI.
Variation on DNA microsatellite of Holstein-Friesian dairy cows in Baturaden Dairy Cattle Breeding Center Sumantri, C; Anggraeni, A; Farajallah, A; Perwitasari, D
Indonesian Journal of Animal and Veterinary Sciences Vol 12, No 2 (2007)
Publisher : Indonesian Animal Sciences Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (134.729 KB) | DOI: 10.14334/jitv.v12i2.550

Abstract

Eight microsatellite loci of which the locations were three on chromosome 6 (BTA6) namely CSN 3, BM 143 and BM 415; two on chromosome 9 (BTA9) namely ETH 225 and BM 4208; and three on chromosome 10 (BTA10) namely BP 31, BM 1237 and BM 888 were used to investigate genotypic variation of Holstein-Friesian (HF) dairy cows in Baturraden Dairy Cattle Breeding Centre. Research activities were carried out through some steps involving blood collection, DNA isolation, amplification on DNA fragments by polymerase chain reaction (PCR) and separation by electrophoresis with silver staining. Frequency and heterozygosity of genes under consideration were calculated. The results showed that the eight microsatellite loci exhibited a total number of 33 alleles. Locations of those alleles were five in BM 143 and BM 4208 loci; four in BM 415, CSN 3, ETH 225, BM 1237, BM 888 loci; and three in BP 31 locus. A number of 14 out of 33 alleles might be specific alleles for HF dairy cattle in Baturraden Dairy Cattle Breeding Centre. The lowest heterozygosity per locus (ĥ) was 0.6151 for BM 415 whilst the highest one was 0.7301 for BM 888. Additionally, the average heterozygosity for all loci (Ĥ) detected in this study was 0.6768. The genotype BB on locus BM 143 and AC on locus CSN-3 significantly affected (P<0.05) the estimated breeding value of milk yield of HF cows in this location. Key Words: Holstein-Friesian Cows, DNA Microsatellite, Allele, EBV of Milk Yield
Molecular characterization of six sub population Indonesian local goats based on mitochondrial DNA D-loop Batubara, Aron; Noor, R.R.; Farajallah, A.; Tiesnamurti, B.; Doloksaribu, M.
Indonesian Journal of Animal and Veterinary Sciences Vol 16, No 1 (2011)
Publisher : Indonesian Animal Sciences Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (136.805 KB) | DOI: 10.14334/jitv.v16i1.634

Abstract

Indonesian local goats were spread in some region, but there was still limited data’s known about the characteristics of its genetic diversity and origin. The Mitochondrial DNA D-loop sequences were used to study the genetic diversity and relationships of six sub population Indonesian local goats, namely, Kacang, Marica, Samosir, Jawarandu, Muara and Bengali goats. From 539 blood samples and DNA extraction collections were selected about 60 samples (10 samples each sub populations) analyzed by PCR-RFLP methods, followed sequence analyzed about 5 PCR products each sub population. The results of the sequence analyses were edited and acquired about 957 bp of nucleotides length. After the alignment analyses were found 50 polymorphic sites which divided into 19 haplotype groups of mtDNA D-loop region. The value of nucleotide diversity was 0.014 ± 0.002. Analysis of Neighbour Joining with Kimura 2 Parameter methods and bootstrap test with 1000 replication indicated that each sub population groups was significantly different between one groups to the others. The maternal lineages origin of six breeds of Indonesian local goats was included to the group of lineage B. The Lineage B was the maternal origin of the haplogroup of goats in the region of East Asia, South Asia, China, Mongolia, North and South Africa, Malaysia, Indonesia, Pakistan and India. Key words: Genetic Diversity, mtDNA D-loop, Haplotypes, Local Goats
Aplication of growth hormone genes familly (GH, GHR, GHRH and Pit-1) for detecting genetic variation of buffaloes in Pandeglang and Lebak districts in Banten Province Sumantri, Cece; Diyono, R; Farajallah, A; Anggraeni, A; Andreas, E
Indonesian Journal of Animal and Veterinary Sciences Vol 15, No 4 (2010)
Publisher : Indonesian Animal Sciences Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (2820.571 KB) | DOI: 10.14334/jitv.v15i4.668

Abstract

Selection using genetic markers are commonly performed to improve livestock productivity in the livestock industry. The objectives of this study were to identify growth hormone genes family (GH|MspI, GH|AluI, GHR|AluI, GHRH|HaeIII and Pit-1|HinfI) polymorphisms of Banten buffalo population consisted of Pandeglang and Lebak subpopulations. A total number of 209 blood samples were collected from 15 districts. Genomic DNAs were extracted by a standard phenol-chloroform protocol and amplified by a polymerase chain reaction (PCR) techniques, then PCR products of GH, GHR, GHRH and Pit-1 Genes were digested with MspI, AluI, HaeIII and HinfI enzyme restriction. Fragments of GH|MspI, GH|AluI, GHR|AluI, GHRH|HaeIII and Pit-1|HinfI were detected by EtBr method. The results showed that GH|MspI and GHRH|HaeIII loci were polymorphic, GH|AluI, GHR|AluI and Pit-1|HinfI, loci were monomorphic. GH allele (-) at locus GH|MspI was only found in Cisata (0.03) and Menes (0.11). Allele B at locus GHRH|HaeIII only found in Cibadak (0.42), Cisata (0.30) and Menes (0.11). In the total population of Banten locus GH|MspI have low diversity (He = 0.02) and polymorphic information content (Pic = 0.02), whereas GHRH|HaeIII locus has a higher diversity (He = 0.23) and Pic (0.22). Key Words: Polymorphism, Growth Hormone Genes, Buffalo
Polymorphism of Calpastatin gene and its effect on body weight of local sheeps Sumantri, C; Diyono, R; Farajallah, A; Inounu, I
Indonesian Journal of Animal and Veterinary Sciences Vol 13, No 2 (2008)
Publisher : Indonesian Animal Sciences Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (470.336 KB) | DOI: 10.14334/jitv.v13i2.604

Abstract

The objectives of this research were to identify polymorphism of calpastatin gene and to investigate any association of calpastatin genotype on body weight of local sheeps. A total number of DNA samples were collected from 288 heads of local sheeps from 8 populations. Two local sheep samples were medium tail sheeps (MTSs) of a Garut fighting type from Ciomas/Bogor (29) and a Garut meat type from Margawati (29). The remaining six local sheep population were one thin tail sheep (TTS) from Jonggol (36); and five fat tail (FTSs) from Indramayu (43), Madura (43), Sumbawa (26), Rote (36) and Donggala (46) respectively. Genomic DNAs of those blood of local sheeps were extracted by a standard phenol-chloroform protocol and amplified using a polymerase chain reaction (PCR) technique. PCR reaction was carried out in a thermocycler (Takara PCR of Thermal Cycler MP4) and PCR products were digested with Msp 1 enzyme restriction using a Restriction Fragment Length Polymorphism (RFLP) technique. The PCR-RFLP products were separated at 8% polyacrylamide gel electrophoresis (PAGE).  A silver-staining method then was applied to detect fragments. Genetic variations between local sheep populations were calculated based on frequencies of genotypes and alelles. The association between genotype of calpastatin gene and body weight of local sheeps were calculated by General Linear Model method by SAS version 6.12. A length of 622 base pairs (bp) of the calpastatin gene of the Indonesian local sheeps was successfully amplified by the PCR technique. An MspI restriction enzyme cut the PCR product into two different length fragments, those were 336 bp and 286 bp designated as M allele of the CAST-Msp1; whilst that unsuccessfully cut PCR product resulted one fragment 622 bp designated as N allele of the CAST-Msp1. Locus of the CAST-Msp1 gene in most local sheeps studied was polymorphic, the exception was in the FTS from Rote of which monomorphic. The highest frequency of the M allele was in the fighting Garut sheep from Ciomas (0.29), whilst the lowest was in the FTS from Rote (0.00). However, frequencies of the M allele of FTSs from Sumbawa and Madura were similar (0.04). Further, frequencies of the M allele of local sheeps from Margawati, Jonggol, Indramayu, and Donggala were 0.24, 0.16, 0.13 and 0.12 respectively. The highest frequency of MN genotype was observed in the Garut fighting sheep from Ciomas (0.58), but the lowest was in the FTS from Rote (0.00). The heterosigosity was observed differently  among populations. The highest heterosigosity was also identified in the Garut fighting sheep in Ciomas (0.43), whilst FTSs both in Sumbawa and Madura were for the lowest (0.08). Results of this study showed that there was a definit association betwen calpastatin genotype and body weight of male sheeps from which the MN genotype significantly related to a higher body weight compared to that of the NN genotype. Key Words : Local Sheeps, Calpastatin Gene, Polymorphism, Live Weight
Co-Authors A Anggraeni A. Anggraeni Agus Alim Hakim Akhsani, Farid AKICHIKA MIKAMI Ali Mashar Amir Hamidy Amir Hamidy AMIR HAMIDY Annawaty Annawaty Annissa Nuridfi Sasmita Arma Aditya Kartika Aron Batubara Aron Batubara Asri Febriana B. Tiesnamurti Bambang Purwantara Bambang Suryobroto Burhanuddin Burhanuddin C Sumantri C. SUMANTRI Cece Sumantri D Perwitasari D. Herdiana D. Rahmat Daisy Wowor Daisy Wowor Daisy Wowor, Daisy Dede Setiadi Devi Sandriliana DEWI APRI ASTUTI DEWI PURNAMA Dwi Sendi Priyono DYAH PERWITASARI -FARAJALLAH E Andreas E. Andreas Eric N. Smith Eric N. Smith Erni Sulistiawati Eryk Andreas H. Nuraini HERA MAHESHWARI I Inounu Imas Batubara Irma Shita Arlyza Jarmuji Jarmuji Jeane Siswitasari Mulyana Joni Setiawan KANTHI ARUM WIDAYATI Khairiza Lubis Koekoeh Santoso KREY KREY Lora purnamasari, Lora Luthfia Nuraini Rahman M. Doloksaribu Mennofatria Boer Meutiya Agustina Meutiya Agustina, Meutiya Mufti Sudibyo Neviaty P Zamani Nirmala Fitria Firdhausi Nisfa Hanim Novita Anggraeni Nurlisa Butet, Nurlisa Person Pesona Renta Pradana, Tengku Gilang Pudji Achmadi R Diyono R.R. Noor Rarah Ratih Adjie Maheswari RIKA RAFFIUDIN Rissa Herawati Ginting Riyanto, Awal Riyanto, Awal Rose Ida Ummah Rudi Alek Wahyudin Silvia Puspitasari Siti Lutvaniyah Slamet Mulyanto Smith, Eric N. Soemarno, Suprayogo Soemarno, Suprayogo TARUNI SRI PRAWAST MIEN KAOMINI ANY ARYANI DEDY DURYADI SOLIHIN TARUNI SRI PRAWASTI TATI NURHAYATI Tengku Gilang Pradana VELLA NURAZIZAH DJALIL Vella Nurazizah Djalil Wahyudin Abd. Karim Yanti Ariyanti Yanti Ariyanti Yusli Wardiatno